Find research datasets worth reusing

FIGURE 4 in Population Structure and Genetic Diversity in Delphinium (Ranunculaceae) Using Scot Molecular Markers

FIGURE 4: WARD tree of SCoT data revealing species delimitation in the Delphinium sp1= D. teheranicum; sp2= D. camptocarpum; sp3= D. lorestanicum; sp4= D. leptocarpum; sp5= D. persicum; sp 6= D. aucheri; sp7= D. anthoroideum; sp8= D. hohenackeri; sp9= D. stocksianum; sp10: D. rugulosum; sp11: D. ambiguum; sp12= D. ajacis; sp13= D. consolida; sp14= D. oliverianum; sp15= D. flavum; sp16= D. trigonelloides; sp17= D. oliganthum; sp18= D. linarioides; sp19= D. paradoxum.

FIGURE. 3 in Population Structure and Genetic Diversity in Delphinium (Ranunculaceae) Using Scot Molecular Markers

FIGURE. 3. Electrophoresis gel of studied ecotypes from DNA fragments produced by SCoT-15. sp1= D. teheranicum; sp2= D. camptocarpum; sp3= D. lorestanicum; sp4= D. leptocarpum; sp5= D. persicum; sp 6= D. aucheri; sp7= D. anthoroideum; sp8= D. hohenackeri; sp9= D. stocksianum; sp10: D. rugulosum; sp11: D. ambiguum; sp12= D. ajacis; sp13= D. consolida; sp14= D. oliverianum; sp15= D. flavum; sp16= D. trigonelloides; sp17= D. oliganthum; sp18= D. linarioides; sp19= D. paradoxum. L = Ladder 100 bp,

FIGURE 2 in Population Structure and Genetic Diversity in Delphinium (Ranunculaceae) Using Scot Molecular Markers

FIGURE 2: PCA plot of morphological characters revealing species delimitation in the Delphinium species; sp1= D. teheranicum; sp2= D. camptocarpum; sp3= D. lorestanicum; sp4= D. leptocarpum; sp5= D. persicum; sp 6= D. aucheri; sp7= D. anthoroideum; sp8= D. hohenackeri; sp9= D. stocksianum; sp10: D. rugulosum; sp11: D. ambiguum; sp12= D. ajacis; sp13= D. consolida; sp14= D. oliverianum; sp15= D. flavum; sp16= D. trigonelloides; sp17= D. oliganthum; sp18= D. linarioides; sp19= D. paradoxum.

FIGURE. 1 in Population Structure and Genetic Diversity in Delphinium (Ranunculaceae) Using Scot Molecular Markers

FIGURE. 1. Map of Iran shows the collection sites and provinces where Delphinium species were obtained for this study; sp1= D. teheranicum; sp2= D. camptocarpum; sp3= D. lorestanicum; sp4= D. leptocarpum; sp5= D. persicum; sp 6= D. aucheri; sp7= D. anthoroideum; sp8= D. hohenackeri; sp9= D. stocksianum; sp10: D. rugulosum; sp11: D. ambiguum; sp12= D. ajacis; sp13= D. consolida

opencc-by-4.0Aug 2022View details →

Prediction of ternary complex structures using molecular dynamics and proteomics

Source code and structural PDBs that went into the Prediction of ternary complex structures using molecular dynamics and proteomics paper.

Fig. 7. Structure bar plots represent-ing K in Morphological and molecular evidence refute a broad circumscription for Pultenaea glabra (Fabaceae: Mirbelieae), with implications for taxonomy, biogeography, and conservation

Fig. 7. Structure bar plots represent-ing K = 3 through 6, showing largely congruent inference of ancestral popu-lations across the K values, with the exception of P. sp. Wolgan Cliffs, the Lees Pinch population of P. sp. Lees Pinch, and P. flexilis and its hybrids with P. glabra. A mixed ancestry of the suspected hybrid individuals was inferred by STRUCTURE analysis.

opencc-by-4.0Jul 2024View details →

Supporting information file of paper [Crystallographic and theoretical study of the atypical distorted octahedral geometry of the metal chromophore of zinc(II) bis((1R,2R)-1,2-diaminocyclohexane) dinitrate (Journal of Molecular Structure 1248 (2022) 131488)]

Supporting information file of third revision of an already accepted and published paper [Crystallographic and theoretical study of the atypical distorted octahedral geometry of the metal chromophore of zinc(II) bis((1R,2R)-1,2-diaminocyclohexane) dinitrate (Journal of Molecular Structure 1248 (2022) 131488)].

opencc-by-4.0Feb 2018View details →

Molecular dynamics simulation trajectory data for "Permeability and ammonia selectivity in aquaporin TIP2;1: linking structure to function"

Trajectories and input files corresponding to entries in Supplementary Table S1.

opencc-by-4.0Mar 2019View details →

Molecular Dynamics Simulation of Aluminium Binding to Amyloid-beta and its Effect on Peptide Structure

MD frames and highest populated clusters, in PDB format

opennotspecifiedJun 2020View details →

FIGURE 5. Secondary structures for the D1–D1 in Morphology and molecular description of Wilmottia koreana sp. nov. (Oscillatoriales, Cyanobacteria) isolated from the Republic of Korea

FIGURE 5. Secondary structures for the D1–D1', Box-B, and V3 helix in the conserved regions of the 16S–23S internal transcribed spacer region: A, F, K,: Wilmottia murrayi KGI28; B, G, L: W. murrayi FBCC-A402; C, H, M: W. murrayi FBCC-A401; D, I, N, S: W. stricta 16PC; and E, J, O: W. koreana FBCC-A812. These structures were drawn considering Machado-de-Lima et al. (2017).

opencc-by-4.0Oct 2024View details →

Unravelling the Molecular Structure and Confining Environment of an Organometallic Catalyst Heterogenized within Amorphous Porous Polymers

Raw data corresponding to Figure 4c of the following publicaiton:  <div> <div> <div>Jabbour, R.; Ashling, C. W.; Robinson, T. C.; Khan, A. H.; Wisser, D.; Berruyer, P.; Ghosh, A. C.; Ranscht, A.; Keen, D. A.; Brunner, E.; Canivet, J.; Bennett, T. D.; Mellot-Draznieks, C.; Lesage, A.; Wisser, F. M. Unravelling the Molecular Structure and Confining Environment of an Organometallic Catalyst Heterogenized within Amorphous Porous Polymers. Angewandte Chemie International Edition 2023, 62 (44), e202310878. <a href="https://doi.org/10.1002/anie.202310878">https://doi.org/10.1002/anie.202310878</a>.</div> </div> </div>

opencc-by-4.0Nov 2024View details →

Molecular dynamics analysis of iPP-polymorphs; a dataset of alpha and beta atomic structures

This is the dataset corresponding to the publication in the Polymer journal: "Molecular dynamics analysis of iPP-polymorphs; Investigating thermal expansion and elastic properties" Authors: H.N. Chávez Thielemann, J.A.W. van Dommelen, L.E. Govaert, M. Hütter Year: 2024   The dataset presented here provides the chemical structures of iPP crystals, including COMPASS forcefield parameters, as follows: α structures were obtained by repeating the crystalline unit cell 4 times in a, 2 times in b, and 4 times in c (comprising 32 chains and 3456 atoms) <ul> <li><a href="https://zenodo.org/records/14048060/files/alpha2.zip?download=1">alpha2.zip</a>: α2  is the unit cell with perfect up-down alternation.</li> <li><a href="https://zenodo.org/records/14048060/files/alpha1.zip?download=1">alpha1.zip</a>: α1 is an α2 but with 50% random up-down alternation.</li> </ul> A X% of regio defects means that X% of the monomers are incorporated with the inverse head-tail order than in a perfect α2 case. Thus, number of atoms and chains remain unvaried. <ul> <li><a href="https://zenodo.org/records/14048060/files/d2p.zip?download=1">d2p.zip:</a> α2 containing 2% of regio defects.</li> <li><a href="https://zenodo.org/records/14048060/files/d4p.zip?download=1">d4p.zip:</a> α2 containing 4% of regio defects.</li> </ul> Vacancy, 31 chains, 3348 atoms: <ul> <li><a href="https://zenodo.org/records/14048060/files/v1.zip?download=1">v1.zip:</a> contains the same α2 but with a vacancy, i.e. a complete chain is missing.</li> </ul> β structures were obtained by repeating the crystalline unit cell 3 times in a, 2 times in b, and 4 times in c (comprising 36 chains and 3888 atoms) <ul> <li><a href="https://zenodo.org/records/14048060/files/beta2.zip?download=1">beta2.zip:</a> β2 structure is a monochiral domain, with purely right-handed chains.</li> <li><a href="https://zenodo.org/records/14048060/files/beta1.zip?download=1">beta1.zip:</a> β1 structure comprises twelve left- and twenty-four right-handed chains.</li> </ul>   File names ended with _img indicates that supplementary images are provided for that structure. In most of the cases, the LAMMPS data files are accompanied by a PDB file for completeness. To download them all including extra files at once, then download the archive file <a href="https://zenodo.org/api/records/14048060/files-archive">14048060.zip.</a>

dryad32/100

Data from: Structural and compositional mismatch between captive and wild Atlantic salmon (Salmo salar) parrs gut microbiota highlights the relevance of integrating molecular ecology for management and conservation methods.

Stocking methods are used in the Province of Quebec to restore Salmo salar populations. However, Atlantic salmon stocked juveniles show higher mortality rates than wild ones when introduced into nature. Hatchery environment, which greatly differs from the natural environment, is identified as the main driver of the phenotypic mismatch between captive and wild parrs. The latter is also suspected to impact the gut microbiota composition, which can be associated with essential metabolic functions for their host. We hypothesized that hatchery raised parrs potentially recruit gut microbial communities that are different from those recruited in the wild. This study evaluated the impacts of artificial rearing on gut microbiota composition in 0+ parrs meant for stocking in two distinct Canadian rivers: Rimouski and Malbaie (Quebec, Canada). Striking differences between hatchery and wild born parrs' gut microbiota suggest that microbiota could be another factor that could impact their survival in the targeted river, since the microbiome is narrowly related to host physiology. For instance, major commensals belonging to Enterobacteriaceae and Clostridiacea from wild parrs' gut microbiota were substituted in captive parrs by lactic acid bacteria from the Lactobacillaceae family. Overall, captive parrs host a generalist bacterial community whereas wild parrs' microbiota is much more specialized. This is the very first study demonstrating extensive impact of captive rearing on intestinal microbiota composition in Atlantic salmon intended for wild population stocking. Our results strongly suggest the need to implement microbial ecology concepts into conservation management of endangered salmon stocks supplemented with hatchery reared parrs.

opencc-zeroDec 2017View details →

dryad32/100

Data from: Defining conservation units with enhanced molecular tools to reveal fine scale structuring among Mediterranean green turtle rookeries

Understanding the connectivity among populations is a key research priority for species of conservation concern. Genetic tools are widely used for this purpose, but the results can be limited by the resolution of the genetic markers in relation to the species and geographic scale. Here, we investigate natal philopatry in green turtles (Chelonia mydas) from four rookeries within close geographic proximity (~ 200km) on the Mediterranean island of Cyprus. We genotyped hypervariable mtSTRs, a mtDNA control region sequence (CR) and 13 microsatellite loci to genetically characterise 479 green turtles using markers with different modes of inheritance. We demonstrated matrilineal stock structure for the first time among Mediterranean green turtle rookeries. This result contradicts previous regional assessments and supports a growing body of evidence that green turtles exhibit a more precise level of natal site fidelity than has commonly been recognised. The microsatellites detected weak male philopatry with significant stock structure among three of the six pairwise comparisons. The absence of Atlantic CR haplotypes and mtSTRs among these robust sample sizes reaffirm the reproductive isolation of Mediterranean green turtles and supports their status as a subpopulation. A power analysis effectively demonstrated that the mtDNA genetic markers previously employed to evaluate regional stock identity were confounded by an insufficient resolution considering the recent colonisation of this region. These findings improve the regional understanding of stock connectivity and illustrate the importance of using suitable genetic markers to define appropriate units for management and conservation.

opencc-zeroDec 2017View details →

FIGURE 59 in A revision of the Pauropsalta annulata Goding & Froggatt species group (Hemiptera: Cicadidae) based on morphology, calling songs and ecology, with investigations into calling song structure, molecular phylogenetic relationships and a case of hybridisation between two subspecies

FIGURE 59. Chronogram showing an estimated phylogeny with divergence times for the Pauropsalta annulata species group, along with outgroups from the tribe Cicadettini, based on CO1 and dynamin data (modelled independently). The topology is a maximum clade credibility from an MCMC search, enforcing a relaxed molecular clock with branch lengths modelled using a GTR + I + G model in *BEAST. Node support is indicated by black closed circles (BPP=1.00) and grey closed circles (BPP=0.95–0.99) from BEAST. Clock calibration is based on a rate of 0.0115s/s/myr for CO1 (see Phylogenetic Analysis Methodology section).

FIGURE 55 in A revision of the Pauropsalta annulata Goding & Froggatt species group (Hemiptera: Cicadidae) based on morphology, calling songs and ecology, with investigations into calling song structure, molecular phylogenetic relationships and a case of hybridisation between two subspecies

FIGURE 55. Results of two Non-metric Multidimensional Scaling ordination analyses using the durations of the four song segments (Fig. 54) for Pauropsalta annulata (red), Pauropsalta tremula (purple), Pauropsalta notialis notialis (orange), Pauropsalta notialis incitata (blue) and Pauropsalta notialis notialisxincitata (green) (n=532). Closed points denote individuals recorded in sympatry with other species in the P. annulata species complex, whereas open outlined points are individuals recorded in allopatry. A cluster analysis revealed five clusters among the data, as indicated, and the composition of each is detailed in the text.

FIGURE 52 in A revision of the Pauropsalta annulata Goding & Froggatt species group (Hemiptera: Cicadidae) based on morphology, calling songs and ecology, with investigations into calling song structure, molecular phylogenetic relationships and a case of hybridisation between two subspecies

FIGURE 52. Male calling song structure of Pauropsalta ayrensis Ewart illustrated in expanded waveform plots (explained in Fig. 8), showing both buzzing and lilting components. The spectrogram at the bottom of the figure displays song frequency, which exhibits no modulation between the song components in this species. This specimen was recorded in the field at Eidsvold (25°22'S 151°07'E).

FIGURE 51 in A revision of the Pauropsalta annulata Goding & Froggatt species group (Hemiptera: Cicadidae) based on morphology, calling songs and ecology, with investigations into calling song structure, molecular phylogenetic relationships and a case of hybridisation between two subspecies

FIGURE 51. Map of eastern Australia showing the geographical distribution of Pauropsalta ayrensis Ewart. Large triangles represent specimen records (see material examined) and small triangles represent aural records (some recorded).

FIGURE 50 in A revision of the Pauropsalta annulata Goding & Froggatt species group (Hemiptera: Cicadidae) based on morphology, calling songs and ecology, with investigations into calling song structure, molecular phylogenetic relationships and a case of hybridisation between two subspecies

FIGURE 50. Waveform plots illustrating the lilting component of the male calling song of Pauropsalta rubristrigata (Goding and Froggatt) from four different localities, including: (i) Penola (37°24'S 140°50'E), (ii) Nimmitabel (36°31'S 149°14'E), (iii) Napoleon Reef (33°26'S149°45'E), and (iv) Woods Reserve (35°28'S 148°57'E). Recording (iv) is shown in two fragments from the same individual recording. Mean phrase repetition rates (PRR) for each recording are provided to the right of each plot for reference. The upper fragment shows the typical lilting component and the lower fragment illustrates a transition into the extended lilting component (a grey dashed line indicates the point of transition). Recording (i) was made with RS6 by B. Haywood, while all other recordings were made by LWP using RS5 (see methods).

FIGURE 49 in A revision of the Pauropsalta annulata Goding & Froggatt species group (Hemiptera: Cicadidae) based on morphology, calling songs and ecology, with investigations into calling song structure, molecular phylogenetic relationships and a case of hybridisation between two subspecies

FIGURE 49. Male calling song structure of Pauropsalta rubristrigata (Goding and Froggatt) illustrated in expanded waveform plots (explained in Fig. 8), showing both buzzing and lilting components. The spectrogram at the bottom of the figure displays song frequency, which exhibits no modulation between the song components in this species. This specimen was recorded in the field at Nimmitabel (36°31'S 149°14'E) using RS5 (see methods).